Litigation forced the dissolution of three major tobacco industry-funded organisations because of their egregious role in spreading scientific misinformation. Yet in 2017, a new scientific organisation—the Foundation for a Smoke-Free World (FSFW)—was launched, funded entirely by tobacco corporation Philip Morris International (PMI). Experts fear FSFW similarly serves to benefit its funder’s scientific and political agenda. We present three case studies of FSFW’s publishing practices to explore: whether FSFW and its affiliates are acting with scientific integrity in their attempts to publish research; how conflicts of interest (COI) are governed in the journals FSFW targets; whether scientific publishing needs to be better protected from the tobacco industry in light of this, and if so, how. FSFW and its grantees have resorted to repeated obfuscation when publishing their science. FSFW staff have failed to act transparently and arguably have sought control over editorial processes (at times facilitated by PR firm, Ruder Finn). FSFW-funded organisations (including its Italian ‘Centre of Excellence’) and researchers affiliated with FSFW (including those working as editors and peer-reviewers) have failed to disclose their links to FSFW and PMI. While journals also failed to apply their COI policies, including on tobacco industry-funded research, the findings highlight that such policies are almost entirely dependent on researchers fully declaring all potential COIs. The paper explores ways to address these problems, including via standardised reporting of COI and funding in journals; journal policies prohibiting publication of tobacco industry-funded science; development of an author-centric database of financial interests; and legally mandated tobacco industry financial contributions to fund science on new tobacco and nicotine products.